Natural ecosystems comprise the planet’s wild plant and
animal resources, but large tracts of land have been converted
to agroecosystems to support the demand for agricultural
products. This conversion limits the number of plant species
and decreases the soil biological diversity. Here we used highthroughput
16S rRNA gene sequencing to evaluate the responses
of soil bacterial communities in long-term converted
and fertilized red soils (a type of Ferralic Cambisol). We observed
that soil bacterial diversity was strongly affected by
different types of fertilization management. Oligotrophic bacterial
taxa demonstrated large relative abundances in chemically
fertilized soil, whereas copiotrophic bacterial taxa were
found in large relative abundances in organically fertilized
and fallow management soils. Only organic-inorganic fertilization
exhibited the same local taxonomic and phylogenetic
diversity as that of a natural ecosystem. However, the
independent use of organic or inorganic fertilizer reduced
local taxonomic and phylogenetic diversity and caused biotic
homogenization. This study demonstrated that the homogenization
of bacterial communities caused by natural-to-agricultural
ecosystem conversion can be mitigated by employing
rational organic-inorganic fertilization managemen
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